title: Fktn-floxed 4

city: Okayama

first: Yuki

last: Katanosaka

address: Shikata-cho 2-7-1

country: Japan

institute: Okayama University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Heart tissue +Tamoxifen 4d

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA Kit (TaKaRa Bio, Shiga, Japan) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop Lite spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

value: Heart

tag: strain

value: male

value: Control


title: ALL54_Dex rep2_RNA-seq

status: Public on Nov 08 2019

type: SRA

city: UNSW Sydney

first: Yizhou

last: Huang

state: NSW

address: High Street

country: Australia

institute: University of New South Wales

description: RNA-seq of ALL54 Dex-treated #2

library_source: transcriptomic

data_processing:
Raw sequencing reads filtered for adapter contamination, low quality scores, and excluded reads in which more than 10% of bases were unknown.
Filtered paired-end RNA-seq reads aligned to the human genome (hg19) using the software package STAR with standard parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization on the UCSC genome browser

molecule: total RNA

organism: Homo sapiens

source_name: ALL xenograft cells

growth_protocol: ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly.

extract_protocol:
Cell suspensions of spleens were prepared and mononuclear cells enriched to >97% human by density gradient centrifugation. The spleen-harvested cells were used for ChIP-seq assay. Lysates were clarified from sonicated nuclei and crosslinked protein-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared by Novogene (Hong Kong) for sequencing using standard Illumina protocols

treatment_protocol: When >70% %huCD45+ engraftment in the peripheral blood was apparent, which occurred 8-10 weeks post-transplantation, mice were treated with either dexamethasone (15 mg/kg) or vehicle control by intra-peritoneal (IP) injection, and culled at 8 hours following the treatment.

tag: tissue

value: ALL xenograft cells

tag: treatment

value: Dex

tag: type

value: Sensitive


title: Expt 6 - DonorB-pDC

type: RNA

city: Baltimore

first: Donald

middle: Welton

last: MacGlashan

state: MD

address: 5501 Hopkins Bayview Circle

department: Allergy and Clinical Immunology

country: USA

institute: Johns Hopkins University

description:
the sample title describes a preparation of cells (Expt xx) and the conditions of treatment and follow naming consistent with the published report
mRNA & miRNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: due to the way data was processed in the published description of these results (no global normalization), the matrix of results that is normally entered as normalized is not normalized but instead a replicate of the non-normalized data

label: biotin

source_name: peripheral blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: 2 forms of preparation: CD34+ cells were cultured in StemPro+supplement or basophils, eosinophils and plasmacytoid dendritic cells were purified from the same donor, same blood draw

extract_protocol: mRNA was isolated by miRNEasy kit extractions and contained both mRNA and miRNA, RIN values > 6 (lower allowed because of presence of miRNA)

treatment_protocol: no treatments were performed, cells in their resting state after preparation

tag: cell type

value: pDendritic Cells:purified to average of 99%


title: Expt 5 - DonorA-pDC


title: Expt 6 - DonorB-eosinophil

value: eosinophils purified to average of 99%


title: Expt 6 - DonorB-basophil

value: basophils:purified to average of 99%


title: Expt 5 - DonorA-eosinophil


title: Fktn-floxed 3

organism: Mus musculus

tag: gender

tag: genotype/variation


title: ALL54_Ctrl rep3_RNA-seq

description: RNA-seq of ALL54 Control #3

value: vehicle


title: Fktn-floxed 2


title: Expt 8 - DonorD-pDC


title: ALL54_Ctrl rep1_RNA-seq

description: RNA-seq of ALL54 Control #1


title: ALL54_Ctrl rep2_RNA-seq

description: RNA-seq of ALL54 Control #2


title: ALL50_Ctrl_Input

description: Input material of ALL50 Control

library_source: genomic

data_processing:
Raw sequencing reads filtered for adapter contamination, low quality scores, and excluded reads in which more than 10% of bases were unknown.
Filtered ChIP-seq reads aligned to the human genome (hg19) using the software package BWA with standard parameters.
Peak calling for GR and CTCF was performed using the software packages HOMER, SPP and MACS2, with peaks detected by at least 2 algorithms considered real peaks.
Peak calling for histone modifications was performed using the software package MACS2 with options to detect broad peaks for histone modifications (--broad) and to filter sites with an adjusted q-value < 0.05 (--broad-cutoff 0.05).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files. Aligned files for UCSC genome browser visualization.

molecule: genomic DNA

extract_protocol:
Cell suspensions of spleens were prepared and mononuclear cells enriched to >97% human by density gradient centrifugation. The spleen-harvested cells were used for ChIP-seq assay. Lysates were clarified from sonicated nuclei and crosslinked protein-DNA complexes were isolated with antibody.
Library preparation was performed by Novogene (Hong Kong) using a variation of the Illumina’s standard protocol. Briefly, the pipeline consists of 3 steps; 1. DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptors; 2. PCR amplification and size selection (usually 100-300bp, including adaptor sequence); 3. Qualified library for cluster preparation and sequencing.

tag: chip antibody


title: 48_HSC_PDGFbb_plus_SHP099_3

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
TopHat v2.1.0 for alignment
FeatureCounts to quantify expression
edgeR for defining differentially expressed genes
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tsv format containing edgeR differential expression results along with RPKM values

source_name: Liver

growth_protocol: Primary human hepatic stellate cells (ScienCell) were maintained in complete media (10% FBS, 1% Peni/Strep). Cells were splited when they reached a maximum of 80% confluence. Cells were cultured up to 8 passages.

extract_protocol: Total RNA was extracted utilizing the RNeasy Mini Kit (Qiagen, #74104).

treatment_protocol: Primary human hepatic stellate cells were treated with 10 ng/mL PDGF or PDGF + 10 µM SHP099 for 48 hours.

value: Liver

value: primary hepatic stellate cells


title: 47_HSC_PDGFbb_plus_SHP099_2


title: ALL50_Dex_Input

description: Input material of ALL50 Dex


title: Expt 5 - DonorA-basophil


title: Expt 2 - CD34(B)-D0

source_name: culture

value: cultured CD34+ cells


title: Fktn-floxed 1


title: Expt 2 - CD34(B)-D21


title: Expt 3 - CD34(C)-D21


title: 45_HSC_PDGFbb_3

value: PDGF


title: Expt 3 - CD34(C)-D0


title: Expt 1 - CD34(A)-D0


title: ALL50_Dex_IgG

description: IgG ChIP-seq of ALL50 Dex

value: IgG


title: Expt 1 - CD34(A)-D21


title: DL2Light

city: Bayreuth

first: Tillmann

last: Lueders

state: Bayern

address: Dr.-Hans-Frisch-Straße 1-3

department: Lehrstuhl Ökologische Mikrobiologie (ÖMIK)

country: Germany

institute: Universitaet Bayreuth

description:
otu_mc2_over0.01per_wtax.biom
KEGG_rel_lvl3
KEGG_rel_lvl4

data_processing:
Demultiplexing was performed with Illumina bcl2fastq (v2.19) and adapters were trimmed with Skewer v.0.2.2 (Jiang et al. 2014)
Paired-end sequences were merged using Adapterremoval (Lindgreen 2012) with parameter -c and default Illumina adapter sequences (since adapters had already been removed). Default settings except: trim ambiguous bases (N) at 5'/3' termini , trim bases at 5'/3' termini with quality scores ≤ 15 and minimum read length of 50.
RNA was sorted into 16S, 23S, and non-rRNA using SortmeRNA v2 (Kopylova et al. 2012) using SSU and LSU databases from Silva v123 (Quast et al. 2013). 16S and non-rRNA reads were then processed separately.
Non-rRNA tags were compared against the KEGG v58.1 database using DIAMOND (Buchfink et al., 2015). Annotations were analyzed using MEGAN 5 (Huson et al., 2007).
16S OTU assignment was performed using QIIME v1.9.1. Preprocessing was performed with commands split_libraries_fastq.py (quality=2, p=0.01), truncate_reverse_primer.py, identify_chimeric_seqs.py (method: usearch61), and filter_fasta.py. OTU calling was performed using the Silva database release 123 using pick_open_reference_otus.py (97 % similarity) and filter_otus_from_otu_table.py .
Genome_build: 16S: Silva database release 123. Functional transcripts: KEGG datavase v58.1
Supplementary_files_format_and_content: 16S: the biom file is the output from OTU assignment with QIIME and contains non-normalized read counts of each OTU. Functional transcripts: the megan file can be imported into MEGAN 5 and contains relativized read counts for each non-rRNA at all levels in the KEGG hierarchy. The text file is an output from MEGAN and includes each functional transcript with its KEGG ID number and relativized read counts from each sample. The MEGAN and text file contain data from samples sequenced on runs 2 and 3 (see characteristic: SeqRun column), which were chosen for analysis in our paper.
Supplementary_files_format_and_content: Note: We sequenced total RNA from each sample, so we got 16S and mRNA from the same sequencing library. However, the mRNA data from some of these libraries (AL1Heavy, AL1Light, AL5Heavy, AL5Light, AU2Light, BL1Heavy, BL1Light, BL5Heavy, BL5Light, BU2Light, CL3Heavy, CL3Light, CL4Heavy, CL4Light) was not sufficiently high quality, so they were not considered during analysis of mRNA. Since rRNA is much more robust against degradation and more abundant in the library data (~ 33%, vs. < 3% of total reads), we included all samples in 16S analysis, but excluded some from mRNA analysis (the results of which are reported in files KEGG_rel_lvl4.txt and Runs23_KEGG-rel.megan).

organism: aquifer metagenome

source_name: Aquifer sediment (Environmental microbial community)

growth_protocol: Each microcosm consisted of a 250 ml serum bottle with 5 g (wet weight) sediment material, 45 ml artificial groundwater medium, and ~5 µL of non-labeled  (12C) or fully labelled (13 463 C7) toluene bound to XAD7 resin beads. Microcosms had an N2/CO2 (80/20, v/v) headspace. There were 4 redox conditions: aerobic (DO ~8 mg/L), microaerobic (DO 0-0.5 mg/L), microaerobic with nitrate (DO 0-0.5 mg/L, nitrate 7.6 mM), and anaerobic (nitrate 7.6 mM), with DO maintainted by daily replenishment with air injected through a 0.2 µm filter. Microcosms were incubated at 12 °C with 145 rpm rotary shaking.

extract_protocol:
RNA was extracted using a bead-beating phenol-chloroform protocol modified from (Schmitt et al. 1990), shaken with a Tissuelyzer II (QIAgen) instead of a beadbeater and precipitated using 1 vol isopropanol and 0.5 vol 7.5 M ammonium acetate.
After isopycnic centrifugation, RNA was converted to double stranded cDNA using the SuperScript IV First-Strand Synthesis System and SuperScript Double-Stranded cDNA Synthesis Kit (Thermofisher). Library preparation was performed using the Nextera XT kit (Illumina) according to manufacturer protocols.

treatment_protocol: RNA was extracted and separated into fractions by isopycnic centrifugations according to Lueders (2015).

tag: redox

value: Anox

tag: fraction

value: Light

tag: isotope

tag: seqrun


title: aMHC-MCM-Fktn-cKO 3

value: Heart


title: aMHC-MCM-Fktn-cKO 2

value: male


title: 44_HSC_PDGFbb_2


title: 43_HSC_PDGFbb_1


title: ALL50_Ctrl_IgG

description: IgG ChIP-seq of ALL50 Control


title: aMHC-MCM-Fktn-cKO 1


title: CU2Light

value: Microox


title: CU1Light


title: HSP90_Input

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
RNA-seq reads were trimmed with TrimGalore (http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/, v0.4.0) and mapped to Gencode (GRCh37, release: 19 or GRCm38, release m4, respectively) annotation using TopHat2 (Kim, Pertea et al. 2013) (v2.0.13) with the options mate- inner-dist, mate-std-dev and library-type (fr- firststrand). The distance between read mates (mate-inner- dist [http://broadinstitute.github.io/picard.] (v1.1.21). After mapping of the RNA-seq reads from all samples, the reads that mapped uniquely to the genome were counted using featureCounts (Liao, Smyth et al. 2014) with the following options: -Q 10 -p -B -C -s 2. The annotations present in the Homo sapiens gtf file from the Ensembl release 75 were used as reference for counting. DESeq2 (Love, Huber et al. 2014) was used for differential expression analysis of all replicates for each condition. Genes with an adjusted P value < 0.01 and absolute log2 fold change more than 1 were defined as significantly affected.
ChIP-seq reads were aligned to the human genome build hg38 or mouse genome mm10, respectively, using Bowtie2 (Langmead and Salzberg 2012). Duplicate and discordant reads were removed. Peak calling was done with MACS2 (model- based analysis of ChIP- Seq) (Zhang, Liu et al. 2008) using "-- keep-dup all", "--nomodel" and "--extsize 200". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 26 and for mouse genome from Gencode annotation release m4. For visualization, the paired-end reads were extended to fragment size and normalized to total reads aligned (reads per million, rpm) using deeptools2 (Ramirez, Ryan et al. 2016). Profile plots and heatmaps of ChIP-seq signal were generated with deeptools2 (Ramirez, Ryan et al. 2016).
Genome_build: hg38 / mm10
Supplementary_files_format_and_content: Text file with raw RNA-seq read counts in Control and upon HSP90 inhibition per cell type.
Supplementary_files_format_and_content: Text file with HSP90 ChIP-seq peaks in K562 cells.

extract_protocol: Chromatin preparation for K652 was performed according to Arrigoni et al., 2016 (Arrigoni, Richter et al. 2016). Chromatin Immunoprecipitation was performed as previously described (Lee, Johnstone et al. 2006).

treatment_protocol: Hsp90 inhibition was carried out using the following concentrations of NVP-AUY922 for 16h hours with the corresponding cell types: 50nM for HPC-7, 200nM for MEFs and 300nM for K562.

tag: cell line

tag: condition

value: Control


title: HSP90_ChIP-seq

value: HSP90B Abcam (ab53497)


title: ALL54_Dex_IgG

description: IgG ChIP-seq of ALL54 Dex

value: ALL xenograft cells

value: Dex


title: 46_HSC_PDGFbb_plus_SHP099_1


title: ALL54_Ctrl_IgG

description: IgG ChIP-seq of ALL54 Control


title: K562_HSP90i_Rep2

extract_protocol: RNA isolation was done using TRI-Reagent (Sigma Aldrich, #T9424) according to manufacturer’s.

value: HSP90 inhibition


title: Expt 1 - CD34(A)-D17(G1 culture method)

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: GCOS 4.0, the normalized and non-normalized data are the same

growth_protocol: 2 forms of preparation: CD34+ cells were cultured in StemPro+supplement+ G1=IL-3(5ng/ml) or G3=IL-3/SCF/Flt3L(5,4,8 ng/ml)


title: CL5Heavy

value: Heavy


title: ALL50_Dex_H3K27Ac

description: H3K27Ac ChIP-seq of ALL50 Dex


title: CL4Light


title: ALL50_Ctrl_H3K27Ac

description: H3K27Ac ChIP-seq of ALL50 Control

value: vehicle


title: C2C12: siSAM

city: HONG KONG

first: Jie

last: Yuan

state: HONG KONG

address: Prince of Wales Hospital

department: Orthopaedics and Traumatology

country: China

institute: The Chinese University of Hong Kong

data_processing:
adaptor sequences and low quality bases on the fragment ends (i.e., quality score < 5) were trimmed
Remaining reads were aligned to the mm9 using the TopHat (v2.0.4) software with the following parameters: transcriptome mismatches= 3; mate-std-dev = 50; genome-read-mismatches = 3; bowtie1; r=0; with the paired-end alignment option as well as the annotated gene model file (refGene for mm9) from  UCSC
expression levels were quantified using Cufflinks with defalt parameters, as well annotated gene model (refGene for mm9) from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files from Cufflinks containing FPKM values

molecule: polyA RNA

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep.

extract_protocol:
Total RNAs were extracted from C2C12 cells using TRIzol reagent (Invitogen) following the manufacturer's instructions and then subjected to poly(A) selection by using mRNA purification beads(Ambion, 61006).
RNA libraries were prepared by using NEBNext® Ultra™ II RNA Library Preparation Kit (NEB, E7770S) and barcoded libraries were pooled at equal concentration and sequenced on the HiSeq1500 platform.

treatment_protocol: C2C12 myoblasts were transfected with siRNA for 48h using  Lipofectamine 2000 reagent.

value: myoblast


title: CL4Heavy


title: 6419c5-Usp22-KOB-no3

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Transcript quantification using Salmon
Differential gene expression using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Transcript quantification using Salmon

source_name: tumor cells from subcutaneously implanted mouse pancreatic tumors

growth_protocol: in vivo implanted tumor

extract_protocol:
RNA extraction from Qiagen Kit
Library was build by a commercial company, Novogene, for mRNA library

value: pancreatic tumor cell

tag: tumor stage

value: late stage pancreatic tumor cells

tag: genotype


title: 6419c5-Usp22-KOA-no3


title: C2C12: siNC


title: 6419c5-Usp22-KOA-no1


title: 6419c5-Usp22-KOA-no2


title: ALL54_Ctrl_H3K27Ac

description: H3K27Ac ChIP-seq of ALL54 Control


title: CL3Light


title: F4_HfSC MASC

city: Valhalla

first: Paul

middle: Allen

last: Lucas

state: NY

address: Macy 008, New York Medical College

department: Orthopaedic Surgery

institute: New York Medical School

description: 3 biological and technical

data_processing:
TopHat for sequenc read alignment and mapping
Cufflinks for sequence read quantification
Cuffdiff for differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

source_name: Human foreskin

growth_protocol: HfSC MASCs at passage 20 were cultured in OptiMEM/EMEM medium containing 5% horse serum until 80% confluent.  HfSCs were placed on serum-free media 24 hours prior to RNA isolation.

extract_protocol:
Total RNA was extracted using the Trizol Reagent protocol followed by the Qiagen RNeasy mini-kit protocol.
Illumina TruSeq LT stranded total RNA library prep kit was used.

treatment_protocol: No treatment applied.

value: Multipotent adult stem cell

tag: passage


title: 6419c5-Usp22-KOB-no2

tag: strain


title: 6419c5-WT-no2

value: WT


title: ALL54_Dex_H3K27Ac

description: H3K27Ac ChIP-seq of ALL54 Dex

tag: tissue


title: 6419c5-WT-no3


title: CL3Heavy


title: ALL50_Dex_H3K27Me3

description: H3K27Me3 ChIP-seq of ALL50 Dex

tag: treatment


title: F3_HfSC MASC

description: 3 biological and technical


title: 6419c5-WT-no1


title: CL5Light


title: BU2Light


title: ALL50_Ctrl_H3K27Me3

description: H3K27Me3 ChIP-seq of ALL50 Control


title: 6419c5-Usp22-KOB-no1


title: BU1Light


title: F2_HfSC MASC

description: 3 biological and technical


title: BL6Light


title: ALL54_Dex_H3K27Me3

description: H3K27Me3 ChIP-seq of ALL54 Dex


title: Input DNA DoxTam

city: Oslo

first: Shixiong

last: Wang

address: Gaustadalléen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

data_processing:
Basecalling with Illumina 1.9 software
FastX Toolkit (0.013) was used to filter out low quality reads, (min. 97% of bases should have quality score of 10). Command: fastq_quality_filter -v -q 10 -p 97 -i  input file -o output file
Quality filtered data was aligned to hg19 assembly with Bowtie 1.1.2. v=2, m=3, k=1.
samtools (1.3.1) was used to convert sam files to bam files, and to remove duplicate in bam files
peaks were called with macs2 (2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genomic coordinates of PAX2 (HA) peaks called in different treatments

source_name: Mamary gland epithelial cell

growth_protocol: MCF-7 cells were cultured in DMEM with 5% FBS

extract_protocol:
MCF-7 chromatin was sonicated and PAX2 bond genomic regions were isolated by using HA tag antibody.
Libraries were prepared by Norwegian sequencing centre and CRUK genomics core facility

treatment_protocol: Cells were treated with doxycycline (50ng/ml) to induce PAX2 oeverexpresson, followed by tamoxifen (1uM) treatment for 6 hours.

value: Breast adenocarcinoma

value: Female

tag: agent

value: doxycycline+ tamoxifen


title: NF66_2 [RNA-seq]

city: Ann Arbor

first: Robert

middle: J

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

data_processing:
Basecalls were performed using CASAVA v1.8.2.
FastQ files were bases were trimmed using cutadapt, removing the universal Illumina adapter base sequence, while hard-clipping the first 13 bp from the 5' end of the reads. Reads shorter than 26 bp were discarded (cutadapt -a AGATCGGAAGAGC -u 13 -m 26).
Reads were aligned and gene-level counts were obtained using RSEM, with the bowtie aligner option, with a seed-length of 26 and allowing for 2 bp mismatches. (rsem-calculate-expression -p 8 --seed-length 26 -bowtie-n 2)
TMM normalization of gene-level counts was performed using the abundance_estimates_to_matrix.pl script from Trinity v2.2.0. (abundance_estimates_to_matrix.pl --est_method RSEM).
Counts data was imported into DESeq2, lowly expressed genes removed (kept if > 1 count per million mapped reads in all replicates of at least one group), and differential expression comparisons were performed.
Genome_build: X. tropicalis genome (v4.1); Xentr41.transcripts.fa
Supplementary_files_format_and_content: Processed data files include gene-level counts matrix (gene.counts.matrix), as well as RSEM output (*.fastq.genes.results_annot.txt) for each sample showing the length, effective length, expected count, transcripts per million reads mapped (TPM), and fragments per kilobase per million reads mapped (FPKM) for each gene.

organism: Xenopus tropicalis

source_name: Brain (POA/hypothalamus/thalamus)

growth_protocol: We obtained wildtype (WT) Xenopus tropicalis frogs from NASCO and reared them in dechlorinated tap water at 25C under a 13L:11D photoperiod, and fed them frog brittle (NASCO, Fort Atkinson, WI) or Sera Micron plankton food (tadpoles only).

extract_protocol:
We isolated total RNA from tadpole brain using Tri Reagent (Sigma-Aldrich, St. Louis, MO) and the Direct-zol RNA kit (Zymogen) following the manufacturers’ instructions. The quality of the RNA was analyzed using a Bioanalyzer.
Total RNA libraries were prepared by the University of Michigan DNA Sequencing Core.

value: Wild type

value: Middle brain region containing preoptic area/hypothalamus/thalamus

tag: developmental stage


title: ALL54_Ctrl_H3K27Me3

description: H3K27Me3 ChIP-seq of ALL54 Control


title: Input DNA Dox

tag: cell type

tag: gender

value: doxycycline


title: NF62_3 [RNA-seq]


title: DoxTam_rep1 ChIP-seq

tag: chip antibody

value: HA tag (abcam:ab9110)


title: ALL54_Dex_H3K4Me3

description: H3K4Me3 ChIP-seq of ALL54 Dex

value: ALL xenograft cells


title: Dox_rep1 ChIP-seq


title: BL5HeavyRep

tag: redox


title: BL5LightRep

tag: fraction

value: Light


title: ALL50_Dex_H3K4Me3

description: H3K4Me3 ChIP-seq of ALL50 Dex

value: Dex


title: ALL50_Ctrl_H3K4Me3

description: H3K4Me3 ChIP-seq of ALL50 Control


title: NF62_2 [RNA-seq]


title: NF62_1 [RNA-seq]


title: NF66_1 [RNA-seq]


title: RNA-seq control2

city: Guangzhou

first: Li

last: Chen

address: No. 58, Zhongshan 2nd Road

institute: The First Affiliated Hospital of Sun Yat-sen University

description: all.counts.exp.txt

data_processing:
RNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
RNA-seq: Hisat2 2.0.4 mapping to reference genome
miRNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) a)10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
miRNA-seq: Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Homo Sapiens miRNA database and GRCH38.p10 genome.
Genome_build: GRCh38 / miRBase 22.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: papillary thyroid cancer cells

extract_protocol:
miRNA-seq: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols
miRNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TPC-1 cells were cocultured with or without PMN-MDSCs for 48h.

value: untreated


title: BL5Light

tag: isotope


title: 7_RPF_R2

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

institute: Sars International Centre for Marine Molecular Biology

data_processing:
Adapter sequences were clipped using fastx_clipper, part of the FASTX Toolkit 0.0.13, with the following parameters: -a AGATCGGAAGAGCACACGTCT -l 20 -c -n -v -Q33 for RPF reads and -a AGATCGGAAGAGCACACGTCT -l 20 -n -v -Q33 for total RNA reads
Reads were trimmed using fastx_trimmer with the following parameters: -Q33 -f 1
Trimmed reads were mapped to O. dioica rRNA and tRNA sequences using bowtie2 version 2.1.0  with the following parameters: -L 20
Reads not mapping to rRNA or tRNA were mapped to the O.dioica reference genome using Tophat 2.0.13 and Genoscope gene model annotations with default parameters
The featureCounts function in the Rsubread R package was used to count reads mapping to exons and to summarise these at the gene level
Genome_build: 1_Assembly_reference_unmasked_v3.0.fa
Supplementary_files_format_and_content: Matrix of read counts for each gene/transcript (row names are Genoscope transcript IDs) and each sample (summing reads from two flow cells for RPF reads);
Please note that the processed data contains publicly available transcript IDs from Genoscope (http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/), in the "Oikopleura_annot_v1.0.gff    file (under Downloads > annotations).

organism: Oikopleura dioica

source_name: release

growth_protocol: Animals were cultured under normal conditions until day 3 when they remained at their day 2 densities and were fed only evening doses to trigger stasis. At day 7 of stasis animals were either collected or transferred to normal density to trigger release from stasis and collected half an hour later.

extract_protocol:
Total RNA was extracted using RNAqueous. Ribosome protected fragments (RPFs) were extracted using the ARTSeq kit from epicentre using the using MicroSpin S-400 column option.  rRNA was depleted from all samples using RiboZero.
Libraries were prepared for sequencing using the ARTSeq kit from epicentre and the included indices were added for multiplex sequencing.

value: Whole animal

value: Day 7 release

tag: molecule subtype

value: Ribosome-protected RNA


title: 8_RPF_S2

source_name: stasis

value: Day 7 stasis


title: NF56_3 [RNA-seq]


title: ALL54_Ctrl_H3K4Me3

description: H3K4Me3 ChIP-seq of ALL54 Control

value: vehicle


title: BL5Heavy

value: Heavy

tag: seqrun


title: 6_RPF_S1


title: ALL50_Dex_H3K9Ac

description: H3K9Ac ChIP-seq of ALL50 Dex


title: NF56_2 [RNA-seq]


title: NF66_3 [RNA-seq]


title: BL6Heavy


title: BL1HeavyRep


title: NF56_1 [RNA-seq]


title: ALL54_Dex_H3K9Ac

description: H3K9Ac ChIP-seq of ALL54 Dex


title: ALL50_Ctrl_H3K9Ac

description: H3K9Ac ChIP-seq of ALL50 Control


title: 4_Total_RNA_S2

value: Total RNA


title: NF50_3 [RNA-seq]


title: BL1Light


title: ALL54_Ctrl_H3K9Ac

description: H3K9Ac ChIP-seq of ALL54 Control


title: NF50_4 [RNA-seq]


title: BL1Heavy


title: AU4Light

value: Oxic


title: AU2Light


title: BL1LightRep


title: HS-3

city: lanzhou

first: jinqiang

last: quan

address: No. 1 Yingmen Village, Anning District

department: College of Animal Science & Technology

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included dirty reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get clean tags, raw reads were further filtered according to the following rules: 1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N); 2) Removing reads without 3’adapters; 3) Removing reads containing 5’adapters; 4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; 5) Removing reads containing ployA in small RNA fragment; 6) Removing reads shorter than 18nt (not include adapters).
All of the clean tags were aligned with small RNAs in GeneBank database(Release 209.0) to identify and remove rRNA,scRNA,snoRNA,snRNA and tRNA.
Meanwhile all of the clean tags were aligned with small RNAs in Rfam database(11.0) to identify and remove rRNA,scRNA,sonRNA,snRNA and tRNA.
All of the clean tags were also aligned with reference genome. Those mapped to exons or introns might be fragments from mRNA degradation, so these tags were removed. The tags mapped to repeat sequences were also removed.
All of the unannotated tags were aligned with reference genome. According to their genome positions and hairpin structures predicted by software Mireap_v0.2, the novel miRNA candidates were identified. The default parameters of software Mireap_v0.2 were as follows: 1) For animals: 1. Minimal miRNA sequence length is 18nt 2. Maximal miRNA sequence length is 26nt 3. Minimal miRNA reference sequence length is 20nt 广州基迪奥生物科技有限公司 http://www.genedenovo.com/ 4. Maximal miRNA reference sequence length is 24nt 5. Minimal depth of Drosha/Dicer cutting site is 3 6. Maximal copy number of miRNAs on reference is 20 7. Maximal free energy allowed for a miRNA precursor is 18 kcal/mol 8. Maximal space between miRNA and miRNA* is 35nt 9. Minimal space between miRNA and miRNA* is 14nt 10. Maximal bulge between miRNA and miRNA* is 4nt 11. Maximal asymmetry of miRNA/miRNA* duplex is 5nt 12. Flank sequence length of miRNA precursor is 10nt
Genome_build: Oncorhynchus mykiss Omyk_1.0
Supplementary_files_format_and_content: tab-delimited text files include read count and TPM values for each Sample.

organism: Oncorhynchus mykiss

source_name: liver tissues _heat stress

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
After total RNA was mixed, rRNAs were removed to retain mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters.

treatment_protocol: Fish with a mean weight 200 ± 5.5 g were transferred into a 6000 L aerated water tank and were cultured at 18 °C for seven days. Prior to the experiment, the fish were randomly divided into two groups in 500 L water tanks, and allowed to acclimate for another seven days. To simulate temperature conditions in natural environment, the water temperature in the heat stress groups was increased from 18 °C to 24 °C at a constant rate of 1 °C per 24 h using a temperature control system. After anesthetizing with a lethal dose of MS-222 (Sigma Aldrich Co., St. Louis, USA), the liver were harvested from twelve female fishes from both the 18 °C control group and the 24 °C heat stress group. Tissues were immediately flash frozen in liquid nitrogen and stored at −80 °C for gene expression profiling analysis.

value: 24 degrees C

value: liver

tag: age

value: 150 day


title: ALL54_Dex_GR

description: GR ChIP-seq of ALL54 Dex

value: GR


title: ALL54_Ctrl_GR

description: GR ChIP-seq of ALL54 Control


title: 1_Total_RNA_R1


title: 2_Total_RNA_S1


title: ALL50_Ctrl_GR

description: GR ChIP-seq of ALL50 Control


title: Cntrl_rep2

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

country: United Kingdom

institute: Cambridge University

data_processing:
Library strategy: PARE
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed, followed by removing Mme1 restriction enzyme site.
The files were converted from redundant to non-redundant format.
The reads were matched to the reference genome and the construct allowing 0 mis-matches using PatMaN [Prueffer et al.2008].
The degradome reads abundances in the four samples were normalized using RPM [Mortazavi et al. 2008].
Genome_build: Ntab-BX
Supplementary_files_format_and_content: *csv: Comma-separated text files include sequences and raw abundances.

organism: Nicotiana tabacum

source_name: leaves challenged with ToLCNDV

growth_protocol: Nicotiana tabacum was grown in culture room at temperature 25C.

extract_protocol:
Leaf sample challenged with ToLCNDV, followed by infiltration with TRiV-AC2, were isolated at 6 days post infiltration. For control, top leaf were extracted at 16dpi challenging ToLCNDV. RNA were isolated using TRIZOL reagent.
Libraries were constructed in replicate for both treatment and control samples.

treatment_protocol: Nicotiana tabacum leaves were challenged with ToLCNDV, followed by infiltration with TRiV-AC2 construct at 10dpi to the young emerging leaf. For control, Nicotiana tabacum leaves were challenged with ToLCNDV.

value: leaf

tag: infection

value: Tomato leaf curl New Delhi virus (ToLCNDV)

tag: ata-sirna

value: mock


title: Cntrl_rep1


title: 3_Total_RNA_R2


title: AL6Heavy


title: ALL50_Dex_CTCF

description: CTCF ChIP-seq of ALL50 Dex

value: ALL xenograft cells

value: Dex

value: CTCF


title: AL5Light

value: Light


title: AC2_rep2

source_name: leaves challenged with ToLCNDV, followed by infiltration with TRiV-AC2


title: ALL50_Ctrl_CTCF

description: CTCF ChIP-seq of ALL50 Control


title: ALL50_Dex_GR_ChIP4

description: GR ChIP-seq of ALL50 Dex


title: AC2_rep1


title: NF50_1 [RNA-seq]

tag: genotype

value: Wild type

value: Middle brain region containing preoptic area/hypothalamus/thalamus


title: AL5Heavy


title: 5_RPF_R1

value: Whole animal

value: Day 7 release

value: Ribosome-protected RNA


title: AL1Light

value: Oxic


title: AL6Light


title: AC2_sRNA2

description: HD sRNA-seq

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format.
The reads were matched to the reference genome and the construct allowing 0 mis-matches using PatMaN [Prueffer et al. 2008].
The sRNA abundances in the two replicates were normalized using RPM [Mortazavi et al. 2008].
Genome_build: Ntab-BX
Supplementary_files_format_and_content: *csv: Comma-separated text files include sequences and raw abundances.

source_name: leaves infiltrated with ata-siRNA targeting AC2 of ToLCNDV

extract_protocol:
Leaf sample infiltrated with TRiV-AC2 were extracted at 6 days post inoculation. Total RNA was isolated using TRIZOL reagent.
Small RNA libraries, using HD adapters [Sorefan et al. 2012], were made in replicate.

treatment_protocol: Nicotiana tabacum leaf were infiltrated with TRiV-AC2 construct.


title: ALL54_Dex_CTCF

description: CTCF ChIP-seq of ALL54 Dex

source_name: ALL xenograft cells


title: AC2_sRNA1

description: HD sRNA-seq


title: ALL54_Ctrl_CTCF

description: CTCF ChIP-seq of ALL54 Control

value: vehicle


title: AL1Heavy

value: Heavy


title: WT polysome fractionation monosomal fractions timepoint 11

status: Public on Nov 07 2019

city: Oxford

first: Jack

middle: Edward

last: Feltham

state: Oxfordshire

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during early HOC (+40 min from minimum O2%)
column header in processed data file:
p40_mono
WT-sucrose-fractionation_counts.csv

data_processing:
Data was aligned to a combined cerevisiae/pombe genome using STAR
Unique reads were extracted using samtools and converted to .bed format.
Counts tables were generated using custom R scripts.
Genome_build: SacCer3 + ASM294v2
Supplementary_files_format_and_content: counts tables (.csv)
Library strategy: polysome fractionation

organism: Saccharomyces cerevisiae

growth_protocol: Cells were inocluated into a Bioflo320 fermenter containing 1.1 l YMC-YE media maintained at pH 3.5. Cells were grown to saturation (OD600~ 16.0), starved for >2 hrs then fed fresh YMC-YE at 1.5/1.2 ml/min to induce metabolic cycling.

extract_protocol:
Harvested cells were lysed using a Roche MagnaLyser and 2 mg clarified cell lysate was fractionated using a 7-47% sucrose gradient. Fractions containing monosomes were taken forward and spiked with 2 ug purified pombe RNA. Total RNA was extracted from the spiked fractions using a miRNeasy kit (Qiagen).
Libraries were constructed using the Lexogen 3’end Seq kit for Ion Torrent.

treatment_protocol: Dissolved oxygen levels in the chamber were monitored and samples were taken at time intervals relative to the point of lowest dissolved oxygen for a particular cycle.

tag: strain

value: CENPK113-7D rpb3-FLAG

value: Metabolic cycling at 1.2 ml/min in 1.1l vessel


title: WT polysome fractionation monosomal fractions timepoint 9

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during late HOC (+20 min from minimum O2%)
column header in processed data file:
p20_mono
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation monosomal fractions timepoint 10

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during early LOC (+30 min from minimum O2%)
column header in processed data file:
p30_mono
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 8

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during mid HOC (+10 min from minimum O2%)
column header in processed data file:
p10_input
WT-sucrose-fractionation_counts.csv

extract_protocol:
Harvested cells were lysed using a Roche MagnaLyser and 200 ug clarified cell lysate was taken forward and spiked with 6 ug purified pombe RNA. Total RNA was extracted from the cell lysate using a miRNeasy kit (Qiagen).
Libraries were constructed using the Lexogen 3’end Seq kit for Ion Torrent.


title: WT polysome fractionation monosomal fractions timepoint 8

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during mid HOC (+10 min from minimum O2%)
column header in processed data file:
p10_mono
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 9

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during late HOC (+20 min from minimum O2%)
column header in processed data file:
p20_input
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 11

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during early HOC (+40 min from minimum O2%)
column header in processed data file:
p40_input
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 10

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during early LOC (+30 min from minimum O2%)
column header in processed data file:
p30_input
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation monosomal fractions timepoint 1

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during late LOC (-60 min from minimum O2%)
column header in processed data file:
m60_mono
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation monosomal fractions timepoint 4

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during early HOC (-30 min from minimum O2%)
column header in processed data file:
m30_mono
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation monosomal fractions timepoint 7

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during mid HOC (0 min from minimum O2%)
column header in processed data file:
p0_mono
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 5

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during Early HOC (-20 min from minimum O2%)
column header in processed data file:
m20_input
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation monosomal fractions timepoint 5

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during Early HOC (-20 min from minimum O2%)
column header in processed data file:
m20_mono
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 6

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during mid HOC (-10 min from minimum O2%)
column header in processed data file:
m10_input
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation monosomal fractions timepoint 3

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during late LOC (-40 min from minimum O2%)
column header in processed data file:
m40_mono
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation monosomal fractions timepoint 2

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions  of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during late LOC (-50 min from minimum O2%)
column header in processed data file:
m50_mono
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 7

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during mid HOC (0 min from minimum O2%)
column header in processed data file:
p0_input
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 4

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during early HOC (-30 min from minimum O2%)
column header in processed data file:
m30_input
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 3

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during late LOC (-40 min from minimum O2%)
column header in processed data file:
m40_input
WT-sucrose-fractionation_counts.csv


title: CG-2

source_name: liver tissues_control

value: 18 degrees C

tag: tissue

value: liver

value: 150 day


title: CG-1

tag: treatment


title: WT polysome fractionation input timepoint 2

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during late LOC (-50 min from minimum O2%)
column header in processed data file:
m50_input
WT-sucrose-fractionation_counts.csv


title: WT polysome fractionation input timepoint 1

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the input lysate of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during late LOC (-60 min from minimum O2%)
column header in processed data file:
m60_input
WT-sucrose-fractionation_counts.csv


title: HS-1

value: 24 degrees C


title: CG-3


title: HS-2


title: xrn1D 3’-end Seq timepoint 25

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid HOC (-10 min from minimum O2%)
column header in processed data file:
t=_p185_OR_m10min
xrn1D-3’end_seq-counts.csv

data_processing:
Data was aligned to a combined cerevisiae/pombe genome using STAR
Unique reads were extracted using samtools and converted to .bed format.
Counts tables were generated using custom R scripts.
Genome_build: SacCer3 + ASM294v2
Supplementary_files_format_and_content: counts tables (.csv)

source_name: xrn1D 3’-end Seq timepoint 25

extract_protocol:
Harvested cells were spiked with a fixed volume of S. pombe slurry and total RNA was extracted.
Libraries were constructed using the Lexogen 3’end Seq kit for Ion Torrent.

value: CENPK113-7D xrn1D

value: Metabolic cycling at 1.5 ml/min in 1.1l vessel


title: xrn1D 3’-end Seq timepoint 24

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during early HOC (-15 min from minimum O2%)
column header in processed data file:
t=_p180_OR_m15min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 24


title: WT polysome fractionation monosomal fractions timepoint 6

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from the monosomal fractions of a 7-47% sucrose gradient column of cycling CENPK113-7D rpb3-FLAG during mid HOC (-10 min from minimum O2%)
column header in processed data file:
m10_mono
WT-sucrose-fractionation_counts.csv


title: xrn1D 3’-end Seq timepoint 27

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid HOC (+0 min from minimum O2%)
column header in processed data file:
t=_p195_OR_m0min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 27


title: xrn1D 3’-end Seq timepoint 26

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid HOC (-5 min from minimum O2%)
column header in processed data file:
t=_p190_OR_m5min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 26


title: xrn1D 3’-end Seq timepoint 22

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during early HOC (-25 min from minimum O2%)
column header in processed data file:
t=_p170_OR_m25min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 22


title: xrn1D 3’-end Seq timepoint 20

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during late LOC (-35 min from minimum O2%)
column header in processed data file:
t=_p160_OR_m35min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 20


title: xrn1D 3’-end Seq timepoint 17

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during late LOC (-60 min from minimum O2%)
column header in processed data file:
t=_p135_OR_m60min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 17


title: xrn1D 3’-end Seq timepoint 15

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid LOC (+105 min from minimum O2%)
column header in processed data file:
t=_p105min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 15


title: xrn1D 3’-end Seq timepoint 12

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during early LOC (+60 min from minimum O2%)
column header in processed data file:
t=_p60min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 12


title: xrn1D 3’-end Seq timepoint 9

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during early LOC (+30 min from minimum O2%)
column header in processed data file:
t=_p30min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 9


title: xrn1D 3’-end Seq timepoint 2

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid HOC (-5 min from minimum O2%)
column header in processed data file:
t=_m5min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 2


title: xrn1D 3’-end Seq timepoint 1

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid HOC (-10 min from minimum O2%)
column header in processed data file:
t=_m10min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 1


title: xrn1D 3’-end Seq timepoint 6

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during late HOC (+15 min from minimum O2%)
column header in processed data file:
t=_p15min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 6


title: WT 3’-end Seq timepoint 21

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid LOC (+129 min from minimum O2%)
column header in processed data file:
WT_t21
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 21


title: xrn1D 3’-end Seq timepoint 23

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during early HOC (-20 min from minimum O2%)
column header in processed data file:
t=_p175_OR_m20min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 23


title: xrn1D 3’-end Seq timepoint 3

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid HOC (0 min from minimum O2%)
column header in processed data file:
t=_0min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 3


title: xrn1D 3’-end Seq timepoint 16

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid LOC (+120 min from minimum O2%)
column header in processed data file:
t=_p120min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 16


title: xrn1D 3’-end Seq timepoint 21

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during early HOC (-30 min from minimum O2%)
column header in processed data file:
t=_p165_OR_m30min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 21


title: WT 3’-end Seq timepoint 16

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during early LOC (+38 min from minimum O2%)
column header in processed data file:
WT_t16
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 16


title: WT 3’-end Seq timepoint 18

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid LOC (+59 min from minimum O2%)
column header in processed data file:
WT_t18
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 18


title: xrn1D 3’-end Seq timepoint 19

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during late LOC (-40 min from minimum O2%)
column header in processed data file:
t=_p155_OR_m40min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 19


title: WT 3’-end Seq timepoint 15

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during early LOC (+28 min from minimum O2%)
column header in processed data file:
WT_t15
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 15


title: xrn1D 3’-end Seq timepoint 18

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during late LOC (-50 min from minimum O2%)
column header in processed data file:
t=_p145_OR_m50min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 18


title: xrn1D 3’-end Seq timepoint 8

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during early LOC (+25 min from minimum O2%)
column header in processed data file:
t=_p25min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 8


title: xrn1D 3’-end Seq timepoint 13

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid LOC (+75 min from minimum O2%)
column header in processed data file:
t=_p75min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 13


title: xrn1D 3’-end Seq timepoint 11

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during early LOC (+50 min from minimum O2%)
column header in processed data file:
t=_p50min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 11


title: WT 3’-end Seq timepoint 17

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during early LOC (+48 min from minimum O2%)
column header in processed data file:
WT_t17
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 17


title: xrn1D 3’-end Seq timepoint 14

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid LOC (+90 min from minimum O2%)
column header in processed data file:
t=_p90min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 14


title: xrn1D 3’-end Seq timepoint 10

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during early LOC (+40 min from minimum O2%)
column header in processed data file:
t=_p40min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 10


title: xrn1D 3’-end Seq timepoint 7

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during late HOC (+20 min from minimum O2%)
column header in processed data file:
t=_p20min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 7


title: xrn1D 3’-end Seq timepoint 4

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid HOC (+5 min from minimum O2%)
column header in processed data file:
t=_p5min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 4


title: xrn1D 3’-end Seq timepoint 5

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D xrn1D during mid HOC (+10 min from minimum O2%)
column header in processed data file:
t=_p10min
xrn1D-3’end_seq-counts.csv

source_name: xrn1D 3’-end Seq timepoint 5


title: WT 3’-end Seq timepoint 22

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during late LOC (+151 min from minimum O2%)
column header in processed data file:
WT_t22
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 22


title: WT 3’-end Seq timepoint 20

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid LOC (+106 min from minimum O2%)
column header in processed data file:
WT_t20
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 20


title: WT 3’-end Seq timepoint 19

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid LOC (+82 min from minimum O2%)
column header in processed data file:
WT_t19
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 19


title: WT 3’-end Seq timepoint 14

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during early LOC (+22 min from minimum O2%)
column header in processed data file:
WT_t14
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 14


title: WT 3’-end Seq timepoint 13

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during late HOC (+19 min from minimum O2%)
column header in processed data file:
WT_t13
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 13


title: WT 3’-end Seq timepoint 11

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid HOC (+7 min from minimum O2%)
column header in processed data file:
WT_t11
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 11


title: WT 3’-end Seq timepoint 10

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid HOC (+5 min from minimum O2%)
column header in processed data file:
WT_t10
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 10


title: WT 3’-end Seq timepoint 4

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during early HOC (-22 min from minimum O2%)
column header in processed data file:
WT_t4
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 4


title: WT 3’-end Seq timepoint 3

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during early HOC (-27 min from minimum O2%)
column header in processed data file:
WT_t3
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 3


title: WT 3’-end Seq timepoint 8

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid HOC (-7 min from minimum O2%)
column header in processed data file:
WT_t8
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 8


title: WT 3’-end Seq timepoint 7

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid HOC (-12 min from minimum O2%)
column header in processed data file:
WT_t7
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 7


title: WT 3’-end Seq timepoint 1

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during late LOC (-38 min from minimum O2%)
column header in processed data file:
WT_t1
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 1


title: WT 3’-end Seq timepoint 6

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during early HOC (-17 min from minimum O2%)
column header in processed data file:
WT_t6
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 6


title: WT 3’-end Seq timepoint 2

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during late LOC (-32 min from minimum O2%)
column header in processed data file:
WT_t2
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 2


title: WT 3’-end Seq timepoint 12

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid HOC (+13 min from minimum O2%)
column header in processed data file:
WT_t12
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 12


title: control B.4 [re-analyzed]

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

description:
46_11_4B_S12
This is duplicated sample record of GSM3926966 for the convenient retrieval of the complete raw data from SRA

data_processing:
Raw data (bcl-files) were demultiplex and the adapter sequences ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCA","AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT") removed with bcl2fastq2 (v2.20.0.422; Illumina).
Fastq-files were trimmed with cutadapt (v.2.2; Martin 2011). Adapter and primer sequences, ambiquos bases (N) and bases with low quality (Phred score<25) were removed.
Trimmed reads (>25 bp) were mapped to the reference genome (GRCh38) with STAR (v.2.5.3; Dobin et al., 2013).
The read counts for genes were extracted with Rsubreads (v.1.32.4; Liao et al., 2013), excluding duplicates, multimapping reads, chimeric fragments, and reads with mapping quality below 10.
Differential gene expression was analysed with DESeq2 (v.1.22.2; Love et al., 2014), comparing knockout vs WT control. Genes with low reads depth (<50 reads in total) were excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt (Counts_DESeq2_results_CHCHD2.txt.gz)

growth_protocol: Guo et al 2017, total differentiation time: 37days

extract_protocol:
Lysates were extracted directly from plates with the Macherey Nagel Nucleospin RNA extraction kit
NEBNext II Ultra Directional and polyA purification

tag: cell line

value: IPSC derived motor neuron

tag: genotype/variation

tag: replicate


title: WT 3’-end Seq timepoint 9

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during mid HOC (+1 min from minimum O2%)
column header in processed data file:
WT_t9
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 9


title: WT 3’-end Seq timepoint 5

description:
polyA RNA (3’-end)
A 3’-end Seq library generated from cycling CENPK113-7D rpb3-FLAG during late LOC (-19 min from minimum O2%)
column header in processed data file:
WT_t5
WT-3’end_seq-counts.csv

source_name: WT 3’-end Seq timepoint 5


title: IMR32_mock

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of empty vector

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: neuroblastoma

growth_protocol: Human neuroblastoma cell line IMR32 was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The circ-CUX1 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of puromycin.

value: stably transfected with empty vector

value: neuroblastoma

tag: passages


title: IMR32_circCUX1

description: Gene expression after stable transfection of circ-CUX1

value: stably transfected with circ-CUX1


title: control B.1 [re-analyzed]

description:
46_11_1B_S9
This is duplicated sample record of GSM3926963 for the convenient retrieval of the complete raw data from SRA

tag: cell type


title: control B.2 [re-analyzed]

description:
46_11_2B_S10
This is duplicated sample record of GSM3926964 for the convenient retrieval of the complete raw data from SRA


title: control A.2 [re-analyzed]

description:
46_11_2A_S2
This is duplicated sample record of GSM3926960 for the convenient retrieval of the complete raw data from SRA


title: control A.3 [re-analyzed]

description:
46_11_4A_S3
This is duplicated sample record of GSM3926961 for the convenient retrieval of the complete raw data from SRA


title: knockout.CHCHD2.4

tag: knockout gene


title: knockout.CHCHD2.3


title: control A.1 [re-analyzed]

description:
46_11_1A_S1
This is duplicated sample record of GSM3926959 for the convenient retrieval of the complete raw data from SRA


title: knockout.CHCHD2.2


title: knockout.CHCHD2.1


title: control.B.4

data_processing:
Raw data (bcl-files) were demultiplex and the adapter sequences ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCA","AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT") removed with bcl2fastq2 (v2.20.0.422; Illumina).
Fastq-files were trimmed with cutadapt (v.2.2; Martin 2011). Adapter and primer sequences, ambiquos bases (N) and bases with low quality (Phred score<25) were removed.
Trimmed reads (>25 bp) were mapped to the reference genome (GRCh38) with STAR (v.2.5.3; Dobin et al., 2013).
The read counts for genes were extracted with Rsubreads (v.1.32.4; Liao et al., 2013), excluding duplicates, multimapping reads, chimeric fragments, and reads with mapping quality below 10.
Differential gene expression was analysed with DESeq2 (v.1.22.2; Love et al., 2014), comparing knockout vs WT control. Genes with low reads depth (<50 reads in total) were excluded.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt (Counts_DESeq2_results_CHCHD10.txt.gz)


title: control B.3 [re-analyzed]

description:
46_11_3B_S11
This is duplicated sample record of GSM3926965 for the convenient retrieval of the complete raw data from SRA


title: control.B.2


title: control A.4 [re-analyzed]

description:
46_11_6A_S4
This is duplicated sample record of GSM3926962 for the convenient retrieval of the complete raw data from SRA


title: control.B.1


title: control.B.3


title: control.A.4


title: knockout.CHCHD10.B.4


title: control.A.3


title: knockout.CHCHD10.A.2


title: control.A.1


title: knockout.CHCHD10.B.2


title: knockout.CHCHD10.B.1


title: knockout.CHCHD10.A.1


title: knockout.CHCHD10.B.3


title: stroke brain 3

city: Pittsburgh

first: Yejie

last: Shi

state: PA

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

institute: University of Pittsburgh

data_processing:
Genome alignment to GRCm38 using HISAT2 in Chipster v3.15
Counting reads using HTSeq in Chipster v3.15
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv files include read counts for each sample

source_name: brain macrophages

extract_protocol:
Single-cell suspensions were prepared from mouse blood and brain. Peripheral blood was obtained from deeply anesthetized mice by cardiac puncture, and 700 μL of blood was diluted in 1300 μL of HBSS and 100 μL of 1% heparin sodium. The diluted blood was fractioned in 2 mL Ficoll solution at 500 g for 15 min. Mononuclear cells in the middle layer were collected. Mice were transcardially perfused with sterile 0.9% NaCl after blood collection. The ipsilesional brain hemisphere was harvested, and cell suspensions were prepared using the Neural Tissue Dissociation Kit and gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). Suspensions were passed through a 70 μm cell strainer, and fractionated on a 30% and 70% Percoll gradient at 500 g for 30 min. Mononuclear cells at the interface were collected. Isolated mononuclear cells were washed, resuspended at 1×10^6 per mL, and stained with fluorophore-conjugated antibodies and the appropriate isotype controls. Flow cytometry was performed using the FACS Aria I sorter and FACS Diva software (BD Biosciences). Monocytes and macrophages were gated as CD11c–Ly6G–CD11b+CD45high and sorted for bulk RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: procedure

value: stroke

value: brain

tag: cell marker

value: CD11b+ CD45high


title: stroke brain 1


title: stroke blood 2

source_name: blood monocytes

value: blood


title: sham blood 2

value: sham


title: stroke blood 1


title: stroke blood 3


title: stroke brain 2


title: sham blood 3


title: sham blood 1


title: control.A.2


title: GCN5_cKO.RS.R1: GCN5- Round Spermatid Replicate 1

city: Philadelphia

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Alignment: all ATAC-seq paired-end data were aligned to mouse genome assembly GRCm38/mm10 using STAR v2.5.2a with the following parameters: --outFilterMultimapNmax 20 –outFilterMismatchNmax 999 –alignMatesGapMax 1000000
Preprocessing: paired-end alignments were pared down to remove (i) alignments with mates on different chromosomes, (ii) alignments with mates producing a fragment larger than 1kb, and (iii) alignments to the mitochondrial genome. Alignments with multiple alignments of a mate were randomly downsampled to produce a single representative alignment. Fragments of size 180-247 bp were selected to define the mononucleosome fraction of fragments, while fragments < 100 bp in size were selected to define the sub-nucleosome fraction of fragments.
Nucleosome Detection: nucleosome positions were identified using DANPOS v2.1.3 per the previously described settings (Buenrostro et al., 2013).  Briefly, DANPOS was run to detect nucleosome enrichment vs a background of sub-nucleosome enrichment using the following parameters: -p 1 -a 10 -d 20 --clonalcut 0. Resulting spreadsheets were then processed to extract all positions with SMT_Diff_FDR < 0.005 (FDR < 0.5%); loci were centered on the provided locus plus and minus 75 bases to yield the nucleosome position.
Peak Calling: sub-nucleosome sized fragment peaks, which we take to be regions of open chromatin, were called using MACS2 v2.1.0.20140616 with default parameters (no control sample was specified), except that the tag size and the genome size were provided and a q-value threshold was set at 0.1%. Peaks were combined by taking the union of technical repeats and the intersection of biological replicates, merging overlapping peaks. For the SV129 mature sperm, samples SV129.Sp.R1, SV129.Sp.R2, and SV129.Sp.R3 were treated as technical repeats as were samples SV129.Sp.R4, SV129.Sp.R5, and SV129.R6.
Genome_build: mm10
Supplementary_files_format_and_content: All *.Nucleosomes.bed BED files represent nucleosome positions inferred from DANPOS, while all *.Subnucleosome.bed BED files represent regions of open chromatin inferred from MACS

source_name: testes

extract_protocol:
Sexually mature, adult male SV129 mice (8-12wks old, Charles River Laboratories) were humanely euthanized by CO2 asphyxiation according to University of Pennsylvania Institutional Animal Care and Use Committee guidelines.  Immature male germ cells were collected from testes by STAPUT velocity sedimentation as previously optimized, described, and validated by our laboratory (Bryant et al., 2013).  Briefly, for each STAPUT collection testes from 11 adult SV129 mice were dissociated to a single cell suspension with sequential incubation of collagenase (0.9 mg/ml) and trypsin (0.6 mg/ml) with DNase (0.1 µg/ml) in KREBs buffer.  Testes cells were subsequently resuspended in 0.5% BSA and slowly loaded onto a 2-4% BSA gradient.  Cells were allowed to sediment for 105 min prior to fraction collection.  Cell aliquots were stained with DAPI and assessed by fluorescent microscopy for meiotic (M), round spermatid (RS), and elongating/condensing spermatid (ES) fractions.  Cell fractions with at least 85% purity for each stage were pooled, snap frozen, and stored at -80C for further processing.  Mature sperm were collected from the cauda epididymis and incubated in somatic cell lysis buffer (0.1% SDS, 0.5% Triton-X-100) for 15min to remove any non-sperm contaminants.  For each collection the sperm of 11 animals were pooled, counted, and subsequently snap frozen and stored at -80C until further processing. ATAC-seq was performed as previously described(Buenrostro et al., 2013), with slight modifications(Sammons et al., 2015).  Cells were washed with cold PBS, aliquoted (M and Sp: 100k cells/rxn, RS and ES: 200k cells), and centrifuged at 500xg for 10min at 4C in swinging bucket centrifuge.  Following lysis in standard ATAC lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, and 0.1% IGEPAL CA-630), recovered nuclei were tagmented with 2.5U and 5.0U of Tn5 in parallel reactions.
Libraries were amplified for 12 PCR cycles and quantified by KAPA.  Libraries were prepared from two independent STAPUT collections for SV129E cells and 1 STAPUT for Gcn5Ctrl and Gcn5cKO.  Sperm libraries were prepared from individual animals.  All libraries were sequenced on the Illumina NextSeq with paired-end sequencing for 150 cycles.

value: testes

tag: Stage

value: Round Spermatid


title: GCN5_cKO.RS.R2: GCN5- Round Spermatid Replicate 2


title: GCN5_cKO.Sp.R1: GCN5- Mature Sperm Replicate 1

value: Mature Sperm


title: GCN5_cKO.Sp.R2: GCN5- Mature Sperm Replicate 2


title: GCN5_cKO.ES.R2: GCN5- Elongating Spermatid Replicate 2

value: Elongating Spermatid


title: knockout.CHCHD10.A.3


title: knockout.CHCHD10.A.4


title: GCN5_cKO.ES.R1: GCN5- Elongating Spermatid Replicate 1


title: GCN5_WT.Sp.R2: GCN5+ Mature Sperm Replicate 2


title: GCN5_cKO.MS.R2: GCN5- Meiotic Spermatid Replicate 2

value: Meiotic Spermatid


title: GCN5_WT.Sp.R1: GCN5+ Mature Sperm Replicate 1


title: GCN5_WT.RS.R1: GCN5+ Round Spermatid Replicate 1


title: GCN5_WT.ES.R2: GCN5+ Elongating Spermatid Replicate 2


title: GCN5_WT.RS.R2: GCN5+ Round Spermatid Replicate 2


title: SV129.Sp.R5: SV129 Mature Sperm Replicate 5


title: GCN5_WT.MS.R1: GCN5+ Meiotic Spermatid Replicate 1


title: SV129.Sp.R4: SV129 Mature Sperm Replicate 4


title: GCN5_WT.ES.R1: GCN5+ Elongating Spermatid Replicate 1


title: SV129.Sp.R6: SV129 Mature Sperm Replicate 6


title: GCN5_cKO.MS.R1: GCN5- Meiotic Spermatid Replicate 1


title: SV129.ES.R1_1: SV129 Elongating Spermatid Replicate 1 Technical 1


title: SV129.ES.R1_2: SV129 Elongating Spermatid Replicate 1 Technical 2


title: SV129.RS.R2_2: SV129 Round Spermatid Replicate 2 Technical 2


title: SV129.Sp.R1: SV129 Mature Sperm Replicate 1


title: SV129.Sp.R2: SV129 Mature Sperm Replicate 2


title: SV129.ES.R2_2: SV129 Elongating Spermatid Replicate 2 Technical 2


title: SV129.ES.R2_1: SV129 Elongating Spermatid Replicate 2 Technical 1


title: SV129.Sp.R3: SV129 Mature Sperm Replicate 3


title: GCN5_WT.MS.R2: GCN5+ Meiotic Spermatid Replicate 2


title: SV129.RS.R2_1: SV129 Round Spermatid Replicate 2 Technical 1


title: Round Spermatid 0.5U Mnase Replicate 2

data_processing:
Alignment: all paired-end MNase-seq data were aligned to mouse genome assembly GRCm38/mm10 using STAR v2.5.2a with parameters --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignMatesGapMax 1000000
Preprocessing: paired-end alignments were pared down to remove (i) alignments with mates on different chromosomes, (ii) alignments with mates producing a fragment larger than 1kb, and (iii) alignments to the mitochondrial genome. Alignments with multiple alignments of a mate were randomly downsampled to produce a single representative alignment. Fragments of size 180-247 bp were selected to define the mononucleosome fraction of fragments.
Nucleosomes: nucleosome positions were discovered using DANPOS on mononucleosome-sized fragments (parameters -p 1 -a 10 -d 20 --clonalcut 0) and an FDR of 5%.
Genome_build: mm10
Supplementary_files_format_and_content: All BED files represent nucleosome positions inferred from two replicates by DANPOS.

source_name: Round Spermatid 0.5U Mnase

extract_protocol:
Sexually mature, adult male SV129 mice (8-12wks old, Charles River Laboratories) were humanely euthanized by CO2 asphyxiation according to University of Pennsylvania Institutional Animal Care and Use Committee guidelines.  Immature male germ cells were collected from testes by STAPUT velocity sedimentation as previously optimized, described, and validated by our laboratory (Bryant et al., 2013).  Briefly, for each STAPUT collection testes from 11 adult SV129 mice were dissociated to a single cell suspension with sequential incubation of collagenase (0.9 mg/ml) and trypsin (0.6 mg/ml) with DNase (0.1 µg/ml) in KREBs buffer.  Testes cells were subsequently resuspended in 0.5% BSA and slowly loaded onto a 2-4% BSA gradient.  Cells were allowed to sediment for 105 min prior to fraction collection.  Cell aliquots were stained with DAPI and assessed by fluorescent microscopy for meiotic (M), round spermatid (RS), and elongating/condensing spermatid (ES) fractions.  Cell fractions with at least 85% purity for each stage were pooled, snap frozen, and stored at -80C for further processing.  Mature sperm were collected from the cauda epididymis and incubated in somatic cell lysis buffer (0.1% SDS, 0.5% Triton-X-100) for 15min to remove any non-sperm contaminants.  For each collection the sperm of 11 animals were pooled, counted, and subsequently snap frozen and stored at -80C until further processing. SV129 M (105) and RS (2x105) cells were digested with MNase as previously described {Amour:1kr} with slight modifications.  Digestions were carried out with 0U, 0.5U, 1U, or 2U of MNase (Roche) for 7.5min at 37C.  The resulting DNA was phenol:chloroform purified, quantified (Qubit), and tested for quality and correct nucleosomal size distribution with Bioanalzyer DNA 1000 analysis (Agilent).
Sequencing libraries were generated with the NEB Next Ultra II DNA Library Prep Kit for Illumina as described by manufacture protocol.  Libraries were sequenced on the Illumina NextSeq with paired-end sequencing for 75 cycles.

value: 8-12wks old

tag: Sex

value: male

tag: concentration


title: Meiotic Spermatid 1U Mnase Replicate 2

source_name: Meiotic Spermatid 1U Mnase

tag: age


title: Meiotic Spermatid 2U Mnase Replicate 1

source_name: Meiotic Spermatid 2U Mnase


title: Round Spermatid 1U Mnase Replicate 2

source_name: Round Spermatid 1U Mnase


title: Round Spermatid 1U Mnase Replicate 1


title: Meiotic Spermatid 1U Mnase Replicate 1


title: Round Spermatid 2U Mnase Replicate 1

source_name: Round Spermatid 2U Mnase


title: Meiotic Spermatid 0.5U Mnase Replicate 1

source_name: Meiotic Spermatid 0.5U Mnase


title: SV129.MS.R1_1: SV129 Meiotic Spermatid Replicate 1 Technical 1


title: Meiotic Spermatid 0.5U Mnase Replicate 2


title: Meiotic Spermatid 2U Mnase Replicate 2


title: SV129.MS.R2_1: SV129 Meiotic Spermatid Replicate 2 Technical 1


title: SV129.MS.R1_2: SV129 Meiotic Spermatid Replicate 1 Technical 2


title: SV129.RS.R1_1: SV129 Round Spermatid Replicate 1 Technical 1


title: SV129.MS.R2_2: SV129 Meiotic Spermatid Replicate 2 Technical 2


title: Round Spermatid 2U Mnase Replicate 2


title: SV129.RS.R1_2: SV129 Round Spermatid Replicate 1 Technical 2


title: GCN5- Elongating Spermatid Replicate 2

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_cKO.ES.R2

data_processing:
Alignment: all RNA-seq data were aligned to mouse genome assembly NCBI37/mm9 using tophat2 v2.0.11 and parameters --library-type fr-secondstrand --b2-very-sensitive.
Quantitation: tag counts per gene per sample were assessed using HTSeq v0.6.1p1 with parameters -r pos -s yes -t exon -i gene_id.
Adjustment: because we expected a dramatic and global decline in transcription in the later stages of spermatogenesis, the usual RNA-seq quantitative assessments (library size adjustment, or FPKM) were deemed to be inaccurate, as these measurements rely on the assumption that most of the transcriptome does not change with experimental conditions. To obtain a true measurement of expression per gene, ERCC spike-in probes were included in the sequencing reaction, and the alignment index was therefore constructed to contain ERCC spike-in sequences in addition to the assembled mouse chromosomes. Library-size and gene-length adjusted FPKM scores for genes were then corrected by leveraging spike-in data in the following way: for each spike-in probe, the tag ratio at each stage post-meiotic spermatid to meiotic spermatid was computed. This was then compared to the expected spike-in tag ratio, and the “deviation” was defined as the ratio of ratios observed:expected. The average deviation among all ERCC probes in a given stage was called the deviation of the stage. The reciprocal of this coefficient was multiplied by the FPKM scores at that stage to correct for large-scale alterations in the transcriptional landscape. In the event that transcription globally decreases, ERCC spike-in tags become more prominent in the sequencing reaction, thus inflating the observed:expected ratio; multiplying the tag counts by expected/observed therefore deflates the transcriptional read-out to an appropriate level.
Genome_build: mm9
Supplementary_files_format_and_content: Expression Counts.txt has per-sample tag counts for each gene determined by HTSeq, provided for the researcher who wishes to pursue a different adjustment strategy; Spike-In Adjusted FPKMs.txt has adjusted FPKM scores using ERCC spike-in controls for each condition, averaged over replicates.

extract_protocol:
Sexually mature, adult male SV129E mice (8-12wks old, Charles River Laboratories) were humanely euthanized by CO2 asphyxiation according to University of Pennsylvania Institutional Animal Care and Use Committee guidelines.  Immature male germ cells were collected from testes by STAPUT velocity sedimentation as previously optimized, described, and validated by our laboratory (Bryant et al., 2013).  Briefly, for each STAPUT collection testes from 11 adult SV129 mice were dissociated to a single cell suspension with sequential incubation of collagenase (0.9 mg/ml) and trypsin (0.6 mg/ml) with DNase (0.1 µg/ml) in KREBs buffer.  Testes cells were subsequently resuspended in 0.5% BSA and slowly loaded onto a 2-4% BSA gradient.  Cells were allowed to sediment for 105 min prior to fraction collection.  Cell aliquots were stained with DAPI and assessed by fluorescent microscopy for meiotic (M), round spermatid (RS), and elongating/condensing spermatid (ES) fractions.  Cell fractions with at least 85% purity for each stage were pooled, snap frozen, and stored at -80C for further processing.  Mature sperm were collected from the cauda epididymis and incubated in somatic cell lysis buffer (0.1% SDS, 0.5% Triton-X-100) for 15min to remove any non-sperm contaminants.  For each collection the sperm of 11 animals were pooled, counted, and subsequently snap frozen and stored at -80C until further processing. RNA was extracted from all cells using the Qiagen RNAeasy kit.
RNA-seq libraries were prepared using the Script-Seq V2 RNA-seq kit (Illumina) with ribodepletion per manufacturing instructions.  All RNA-seq libraries were sequenced on the Illumina NextSeq with single end sequencing for 75 cycles.

treatment_protocol: Mice with pre-meiotic deletion of Gcn5 in male germ cells were generated by mating Gcn5fl/fl mice (C57BL6), graciously provided by Dr. Sharon Dent (Baylor College of Medicine)(Lin et al., 2008b), with mice expressing Cre recombinase under the control of the Stra8 promoter (FVB/NJ, Jackson Labs, (Sadate-Ngatchou et al., 2008)).  Expression of Stra8-Cre begins at post-natal d3 in early stage spermatogonia, continues through preleptotene stage spermatocytes (Sadate-Ngatchou et al., 2008) and is specific to the male germ line.  Subsequent mixed background F1 Gcn5fl/+; Stra8-Cre+ mice were backcrossed to Gcn5fl/fl mice to generate control (Gcn5fl/+, Gcn5Ctrl) or conditional knock-out mutant animals (Gcn5fl/Δ;Stra8-Cre+, Gcn5cKO) for subsequent experiments.


title: GCN5- Round Spermatid Replicate 2

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_cKO.RS.R2


title: GCN5- Elongating Spermatid Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_cKO.ES.R1


title: GCN5- Mature Sperm Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_cKO.Sp.R1


title: GCN5- Meiotic Spermatid Replicate 2

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_cKO.MS.R2


title: Round Spermatid 0.5U Mnase Replicate 1


title: GCN5+ Elongating Spermatid Replicate 2

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_WT.ES.R2


title: GCN5- Meiotic Spermatid Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_cKO.MS.R1


title: GCN5+ Mature Sperm Replicate 2

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_WT.Sp.R2


title: GCN5- Mature Sperm Replicate 2

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_cKO.Sp.R2


title: GCN5- Round Spermatid Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_cKO.RS.R1


title: GCN5+ Round Spermatid Replicate 2

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_WT.RS.R2


title: GCN5+ Meiotic Spermatid Replicate 2

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_WT.MS.R2


title: IL12_02

city: Ithaca

first: Colleen

last: Lau

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.16-2.19)
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36) and aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Supplementary_files_format_and_content: Text files are raw counts (1 count per pair of reads) calculated using the summarizeOverlaps function from the GenomicAlignments R package (v10.10.1)

source_name: splenic NK cells

extract_protocol:
Cells were sorted directly into Trizol and total RNA underwent amplification using SMART-seq V4 (Clontech) Ultra Low Input RNA kit.
Subsequently, 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on Hiseq 2500 1T, in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 47 million paired reads were generated per sample and the percent of mRNA bases was over to 72% on average.

value: splenic NK cells

value: WT

value: HPOSNEG

tag: condition


title: IL12RWT_HPOS_D2_003

tag: genotype

value: HPOS


title: IL12_01


title: IL12RKO_HPOS_D2_003


title: IL12RWT_HPOS_D2_001


title: IL12RKO_HPOS_D2_002


title: GCN5+ Mature Sperm Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_WT.Sp.R1

tag: strain


title: IL12RWT_HPOS_D2_002

tag: tissue


title: GCN5+ Elongating Spermatid Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_WT.ES.R1


title: GCN5+ Round Spermatid Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_WT.RS.R1


title: SV129 Elongating Spermatid Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
SV129.ES.R1


title: GCN5+ Meiotic Spermatid Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
GCN5_WT.MS.R1


title: SV129 Mature Sperm Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
SV129.Sp.R1


title: SV129 Round Spermatid Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
SV129.RS.R1


title: SV129 Meiotic Spermatid Replicate 1

description:
Spike-In Adjusted FPKMs.txt
Expression Counts.txt
SV129.MS.R1


title: IL12RWT_HPOS_D0_002


title: IL12RKO_HPOS_D0_002


title: IL12RWT_HPOS_D0_001


title: IL12RKO_HPOS_D0_001


title: FAST-PLIN5 ASO-3

city: Minneapolis

first: Douglas

middle: Gene

last: Mashek

state: Minnesota

address: Suite 6-155, 321 Church St. SE

department: Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota

description:
Sample_ID-PA-3_S45
Sample.ID.PA.3
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat2 (v2.0.2) using the mouse genome (mm10) as a reference.
Cuffdiff 2.2.1 was used to quantify the expression level of each known gene in units of FPKM (fragment mapped per kilobase of exons per million mapped reads).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: subread_dmashek: Tab-delimited text file includes feature counts.
Supplementary_files_format_and_content: genes.fpkm_table_dmashek: Tab-delimited text file includes FPKM values.

source_name: Liver

growth_protocol: Purified normal diet.

extract_protocol:
RNA was extracted using the RNeasy Kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CTRL/PLIN5 ASO for gene silence.

value: Liver

tag: aso

tag: feeding

value: Fasted


title: FAST-PLIN5 ASO-5

description:
Sample_ID-PA-5_S47
Sample.ID.PA.5
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: FAST-PLIN5 ASO-4

description:
Sample_ID-PA-4_S46
Sample.ID.PA.4
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: FAST-PLIN5 ASO-2

description:
Sample_ID-PA-2_S44
Sample.ID.PA.2
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: Refed-PLIN5 ASO-3

description:
Sample_ID-A3_S40
Sample.ID.A3
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt

value: Re-fed


title: Refed-PLIN5 ASO-2

description:
Sample_ID-A2_S39
Sample.ID.A2
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: Refed-PLIN5 ASO-4

description:
Sample_ID-A4_S41
Sample.ID.A4
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: FAST-PLIN5 ASO-1

description:
Sample_ID-PA-1_S43
Sample.ID.PA.1
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: Refed-PLIN5 ASO-1

description:
Sample_ID-A1_S38
Sample.ID.A1
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: Refed-1-CTRL ASO-5

description:
Sample_ID-E5_S52
Sample.ID.E5
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt

value: Control


title: Refed-1-CTRL ASO-3

description:
Sample_ID-E3_S50
Sample.ID.E3
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: Refed-1-CTRL ASO-2

description:
Sample_ID-E2_S49
Sample.ID.E2
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: Refed-1-CTRL ASO-4

description:
Sample_ID-E4_S51
Sample.ID.E4
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: FAST-CTRL ASO-1

description:
Sample_ID-PE-1_S53
Sample.ID.PE.1
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: FAST3-CTRL ASO-3

description:
Sample_ID-PE-3_S55
Sample.ID.PE.3
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: FAST5-CTRL ASO-5

description:
Sample_ID-PE-5_S57
Sample.ID.PE.5
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: KO_GV_2

city: shanghai

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

institute: tongji university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.

source_name: Zcchc8 KO_GV oocytes

extract_protocol:
2-5embryos were collected as one replicate. Zona pellucida of embryos were removed with 0.5% protease E (Sigma). Embryos were washed for 5-6 times in 0.5% BSA(Sigma) in PBS solution before put into cell lysis buffer. After incubation at 70°C for 90 seconds, reverse transcription for the first strand cDNA was performed subsequently with a 24 oligo (dT) primer. After second strand cDNA synthesis, cDNA library was amplified for 16-18 cycles based on the embryo number. Amplified cDNA was diluted for 10 times for qPCR reaction.
For library construction, amplified cDNA was sheered to 200-300 bp using Covaris S220 system. The sequence libraries were generated using KAPA HyperPlus Library Preparation kit (Roche, KK8510), following the manufacturer’s instructions. 8-12 cycles amplification was used depending on cDNA concentration.

value: GV oocytes

tag: genotype/variation

value: Zcchc8 KO


title: KO_GV_3


title: Refed-1-CTRL ASO-1

description:
Sample_ID-E1_S48
Sample.ID.E1
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: WT_GV_3

source_name: wild type_GV oocytes

value: wild type


title: KO_GV_1


title: WT_GV_2


title: Refed-PLIN5 ASO-5

description:
Sample_ID-A5_S42
Sample.ID.A5
processed data file: subread_dmashek.txt
processed data file: genes.fpkm_table_dmashek.txt


title: WT_GV_1


title: Zcchc8_RIP_input

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using bowtie2 (v 2.2.9) command with default parameters.
MACS14 (v 1.4.2) with default parameters was used for peak finding.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig file were generated using MACS2(v 2.0.10) pileup function.

extract_protocol:
50 million ES cells over-expressing HA-Zcchc8 and HA-Rbm7 were collected for 0.3% formaldehyde fixation for 10 min. Nuclear pellets were retained after cell lysis for sonication. DNA was sheared between 200-1000bp using Covaris M220 system. 1/50 volume of sheared chromatin was retained as input. Protein A/G magnet beads were incubated with 5ug HA antibody for each reaction. 1/5 volume of sheared chromatin were immunoprecipated with pre-incubated beads overnight. Beads were washed 4 times and eluted (as well as input) following the protocol. Elution samples were cleaned up using RNeasy Mini Kit (QIAGEN).
Purified RNA was used for library construction via KAPA RiboErase Kit, 18 cycles amplification during library construction was used for RIP sample to get the final library. For input RNA, 14 cycles amplification was used.

value: derived ESC

value: HA-tag-Zcchc8 overexpression

tag: rip antibody


title: Zcchc8_RIP_2

value: HA(Proteintech NO:51064-6-AP)


title: Rbm7_RIP_1

value: HA-tag-Rbm7 overexpression

value: HA(Proteintech NO:51064-2-AP)


title: Rbm7_RIP_2

value: HA(Proteintech NO:51064-3-AP)


title: Zcchc8_RIP_1

value: HA(Proteintech NO:51064-5-AP)


title: Rbm7_RIP_input